Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3495505.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3495505.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3495505.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.19, per 1000 atoms: 0.35 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 113.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.93: 636 0.93 - 1.19: 1040 1.19 - 1.45: 691 1.45 - 1.71: 768 1.71 - 1.97: 18 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.461 1.271 0.191 9.20e-03 1.18e+04 4.29e+02 bond pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 1.330 1.574 -0.244 1.26e-02 6.30e+03 3.74e+02 bond pdb=" N BGLU A 64 " pdb=" CA BGLU A 64 " ideal model delta sigma weight residual 1.456 1.686 -0.230 1.22e-02 6.72e+03 3.55e+02 bond pdb=" C ILE A 117 " pdb=" O ILE A 117 " ideal model delta sigma weight residual 1.238 1.455 -0.217 1.17e-02 7.31e+03 3.46e+02 bond pdb=" C BGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 1.335 1.556 -0.221 1.26e-02 6.30e+03 3.08e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.07: 3311 5.07 - 10.15: 1882 10.15 - 15.22: 508 15.22 - 20.29: 73 20.29 - 25.36: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.27 141.39 -19.12 1.23e+00 6.61e-01 2.42e+02 angle pdb=" N ILE A 91 " pdb=" CA ILE A 91 " pdb=" C ILE A 91 " ideal model delta sigma weight residual 110.62 125.23 -14.61 1.02e+00 9.61e-01 2.05e+02 angle pdb=" N PRO A 43 " pdb=" CA PRO A 43 " pdb=" CB PRO A 43 " ideal model delta sigma weight residual 103.25 115.48 -12.23 8.80e-01 1.29e+00 1.93e+02 angle pdb=" C ILE A 21 " pdb=" N PRO A 22 " pdb=" CA PRO A 22 " ideal model delta sigma weight residual 119.19 104.58 14.61 1.06e+00 8.90e-01 1.90e+02 angle pdb=" O GLN A 95 " pdb=" C GLN A 95 " pdb=" N BGLU A 96 " ideal model delta sigma weight residual 122.27 105.71 16.56 1.23e+00 6.61e-01 1.81e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 1308 17.07 - 34.14: 118 34.14 - 51.21: 37 51.21 - 68.28: 16 68.28 - 85.35: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ILE A 21 " pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual -122.00 -146.75 24.75 0 2.50e+00 1.60e-01 9.80e+01 dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 146.95 -24.15 0 2.50e+00 1.60e-01 9.33e+01 dihedral pdb=" N ILE A 21 " pdb=" C ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual 123.40 145.58 -22.18 0 2.50e+00 1.60e-01 7.87e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.247: 116 0.247 - 0.494: 69 0.494 - 0.741: 43 0.741 - 0.988: 12 0.988 - 1.236: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 69 " pdb=" N VAL A 69 " pdb=" C VAL A 69 " pdb=" CB VAL A 69 " both_signs ideal model delta sigma weight residual False 2.44 3.68 -1.24 2.00e-01 2.50e+01 3.82e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.43 -1.16 2.00e-01 2.50e+01 3.36e+01 chirality pdb=" CA BGLU A 94 " pdb=" N BGLU A 94 " pdb=" C BGLU A 94 " pdb=" CB BGLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.64e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.032 2.00e-02 2.50e+03 6.55e-02 1.29e+02 pdb=" CG TYR A 141 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.125 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.096 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.062 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.060 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 172 " -0.051 2.00e-02 2.50e+03 9.56e-02 9.14e+01 pdb=" C LEU A 172 " 0.165 2.00e-02 2.50e+03 pdb=" O LEU A 172 " -0.062 2.00e-02 2.50e+03 pdb=" N ASN A 173 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.067 2.00e-02 2.50e+03 5.22e-02 8.16e+01 pdb=" CG BTYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.076 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.040 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.050 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.002 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.079 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.077 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.042 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 1268 2.35 - 2.91: 8252 2.91 - 3.47: 10473 3.47 - 4.04: 15152 4.04 - 4.60: 21487 Nonbonded interactions: 56632 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.785 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.791 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.808 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.835 2.270 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.836 2.450 ... (remaining 56627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_3495505_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2783 r_free= 0.1849 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.401464 | | target function (ml) not normalized (work): 71492.975600 | | target function (ml) not normalized (free): 3281.685403 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3188 0.2262 7.5043 5.0589| | 2: 3.63 - 2.88 1.00 2711 122 0.2623 0.1733 4.3297 4.3385| | 3: 2.88 - 2.52 1.00 2682 148 0.2557 0.1583 4.1867 4.1873| | 4: 2.52 - 2.29 1.00 2661 139 0.2538 0.1621 3.4876 3.6326| | 5: 2.29 - 2.13 1.00 2678 122 0.2660 0.1500 3.4088 3.467| | 6: 2.13 - 2.00 1.00 2692 117 0.2764 0.1802 3.3294 3.4224| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.64 2819 159 0.88 17.75 0.77 0.23 1332.99| | 2: 3.63 - 2.88 2711 122 0.83 23.99 1.31 0.23 1332.99| | 3: 2.88 - 2.52 2682 148 0.73 33.15 1.29 0.23 1332.99| | 4: 2.52 - 2.29 2661 139 0.93 11.74 1.30 0.26 141.91| | 5: 2.29 - 2.13 2678 122 0.92 14.03 1.32 0.26 141.91| | 6: 2.13 - 2.00 2692 117 0.90 16.71 1.33 0.26 141.91| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 141.91 max = 1332.99 mean = 744.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.97 mean = 19.57| |phase err.(test): min = 0.00 max = 89.67 mean = 19.70| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.278 1557 Z= 5.407 Angle : 5.466 19.351 2118 Z= 3.832 Chirality : 0.408 1.236 243 Planarity : 0.032 0.129 284 Dihedral : 13.528 85.348 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 33.51 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.48), residues: 224 helix: -2.98 (0.36), residues: 109 sheet: -0.21 (0.80), residues: 28 loop : -0.43 (0.61), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.077 0.022 ARG A 156 TYR 0.131 0.041 TYR A 141 PHE 0.124 0.029 PHE A 119 HIS 0.086 0.034 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2783 r_free= 0.1849 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.401464 | | target function (ml) not normalized (work): 71492.975600 | | target function (ml) not normalized (free): 3281.685403 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3087 percent. r_work = 0.2914 r_free = 0.1981 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2860 0.2914 0.1981 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2860 0.2914 0.1981 n_refl.: 17050 remove outliers: r(all,work,free)=0.2149 0.2160 0.1981 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2122 0.2132 0.1963 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1612 0.1610 0.1647 n_refl.: 17045 remove outliers: r(all,work,free)=0.1610 0.1608 0.1647 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3892 398.961 358.943 0.654 1.013 0.397 11.894-9.307 99.02 97 4 0.1845 633.645 615.352 0.930 1.013 0.380 9.237-7.194 100.00 213 7 0.2174 518.258 508.302 0.957 1.013 0.361 7.162-5.571 100.00 427 22 0.2302 388.953 376.423 0.922 1.012 0.294 5.546-4.326 100.00 867 58 0.1397 533.970 529.284 0.964 1.010 0.251 4.315-3.360 100.00 1859 96 0.1292 507.811 503.960 1.015 1.007 0.191 3.356-2.611 100.00 3867 181 0.1648 333.603 329.113 1.011 1.001 0.044 2.608-2.000 99.99 8818 434 0.1645 217.452 213.651 1.028 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4586 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1608 r_free=0.1647 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1609 r_free=0.1648 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.702195 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.954480 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1352 0.1643 0.0291 0.009 1.0 1.0 0.5 0.0 0 11.351 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.43 2.91 3.013 18.450 0.954 0.023 12.76 16.67 3.91 3.696 18.738 0.954 0.020 Individual atomic B min max mean iso aniso Overall: 6.46 113.89 20.02 4.11 1785 0 Protein: 6.46 113.04 17.26 4.12 1519 0 Water: 8.72 113.89 36.06 N/A 258 0 Other: 21.98 37.88 26.76 N/A 8 0 Chain A: 6.46 113.89 20.02 N/A 1785 0 Histogram: Values Number of atoms 6.46 - 17.20 1099 17.20 - 27.95 329 27.95 - 38.69 181 38.69 - 49.43 104 49.43 - 60.18 44 60.18 - 70.92 14 70.92 - 81.66 6 81.66 - 92.40 5 92.40 - 103.15 0 103.15 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1667 r_work=0.1279 r_free=0.1674 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1674 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1273 r_free = 0.1665 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1273 r_free= 0.1665 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019825 | | target function (ls_wunit_k1) not normalized (work): 321.881402 | | target function (ls_wunit_k1) not normalized (free): 27.076512 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1273 0.1665 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1905 0.1903 0.1999 n_refl.: 17043 remove outliers: r(all,work,free)=0.1905 0.1903 0.1999 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1877 0.1874 0.1983 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1291 0.1272 0.1662 n_refl.: 17043 remove outliers: r(all,work,free)=0.1291 0.1272 0.1662 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3547 306.761 287.514 0.652 1.010 0.392 11.894-9.307 99.02 97 4 0.1673 487.209 476.304 0.918 1.010 0.379 9.237-7.194 100.00 213 7 0.1823 398.488 395.864 0.956 1.010 0.341 7.162-5.571 100.00 427 22 0.1833 299.066 294.248 0.930 1.009 0.303 5.546-4.326 100.00 867 58 0.1037 410.569 408.459 0.958 1.007 0.231 4.315-3.360 100.00 1859 96 0.0920 390.455 390.128 1.016 1.005 0.191 3.356-2.611 100.00 3867 181 0.1299 256.507 255.317 1.013 1.000 0.091 2.608-2.000 99.99 8818 434 0.1349 167.198 165.711 1.022 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3773 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1662 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1272 r_free=0.1663 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1663 | n_water=258 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.1280 r_free=0.1648 | n_water=253 | time (s): 20.000 (total time: 20.700) Filter (q & B) r_work=0.1280 r_free=0.1647 | n_water=251 | time (s): 1.650 (total time: 22.350) Compute maps r_work=0.1280 r_free=0.1647 | n_water=251 | time (s): 0.520 (total time: 22.870) Filter (map) r_work=0.1318 r_free=0.1648 | n_water=206 | time (s): 1.610 (total time: 24.480) Find peaks r_work=0.1318 r_free=0.1648 | n_water=206 | time (s): 0.590 (total time: 25.070) Add new water r_work=0.1551 r_free=0.1879 | n_water=364 | time (s): 2.090 (total time: 27.160) Refine new water occ: r_work=0.1339 r_free=0.1599 adp: r_work=0.1276 r_free=0.1590 occ: r_work=0.1280 r_free=0.1555 adp: r_work=0.1245 r_free=0.1560 occ: r_work=0.1245 r_free=0.1548 adp: r_work=0.1234 r_free=0.1551 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1551 r_work=0.1234 r_free=0.1551 | n_water=364 | time (s): 35.960 (total time: 63.120) Filter (q & B) r_work=0.1236 r_free=0.1560 | n_water=356 | time (s): 1.940 (total time: 65.060) Filter (dist only) r_work=0.1237 r_free=0.1559 | n_water=355 | time (s): 28.210 (total time: 93.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.500558 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.967410 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1213 0.1589 0.0375 0.008 0.9 1.9 0.5 0.0 0 12.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 15.89 3.75 4.201 21.127 0.967 0.018 12.01 16.15 4.14 4.227 21.338 0.967 0.018 Individual atomic B min max mean iso aniso Overall: 6.32 107.65 21.27 4.24 1882 0 Protein: 6.32 107.65 17.70 4.23 1519 0 Water: 8.24 65.79 36.28 N/A 355 0 Other: 23.88 42.59 31.74 N/A 8 0 Chain A: 6.32 107.65 19.32 N/A 1733 0 Chain S: 17.89 63.58 43.88 N/A 149 0 Histogram: Values Number of atoms 6.32 - 16.45 1004 16.45 - 26.58 392 26.58 - 36.72 224 36.72 - 46.85 148 46.85 - 56.99 77 56.99 - 67.12 27 67.12 - 77.25 3 77.25 - 87.39 4 87.39 - 97.52 1 97.52 - 107.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1615 r_work=0.1203 r_free=0.1616 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1616 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1613 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1200 r_free= 0.1613 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017113 | | target function (ls_wunit_k1) not normalized (work): 277.839059 | | target function (ls_wunit_k1) not normalized (free): 25.414487 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1200 0.1613 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1817 0.1812 0.1974 n_refl.: 17043 remove outliers: r(all,work,free)=0.1817 0.1812 0.1974 n_refl.: 17043 overall B=-0.51 to atoms: r(all,work,free)=0.1782 0.1776 0.1950 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1195 0.1605 n_refl.: 17043 remove outliers: r(all,work,free)=0.1213 0.1193 0.1605 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3398 306.200 278.584 0.622 1.006 0.370 11.894-9.307 99.02 97 4 0.1452 487.209 483.794 0.917 1.007 0.350 9.237-7.194 100.00 213 7 0.1625 398.488 398.573 0.974 1.006 0.291 7.162-5.571 100.00 427 22 0.1528 299.066 295.965 0.937 1.006 0.273 5.546-4.326 100.00 867 58 0.0877 410.569 407.813 0.958 1.005 0.211 4.315-3.360 100.00 1859 96 0.0836 390.455 389.903 1.014 1.004 0.202 3.356-2.611 100.00 3867 181 0.1212 256.507 255.652 1.008 1.001 0.058 2.608-2.000 99.99 8818 434 0.1331 167.198 166.161 1.010 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1434 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1605 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1605 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1605 | n_water=355 | time (s): 0.810 (total time: 0.810) Filter (dist) r_work=0.1194 r_free=0.1606 | n_water=354 | time (s): 28.470 (total time: 29.280) Filter (q & B) r_work=0.1194 r_free=0.1606 | n_water=354 | time (s): 0.830 (total time: 30.110) Compute maps r_work=0.1194 r_free=0.1606 | n_water=354 | time (s): 0.600 (total time: 30.710) Filter (map) r_work=0.1259 r_free=0.1641 | n_water=257 | time (s): 1.700 (total time: 32.410) Find peaks r_work=0.1259 r_free=0.1641 | n_water=257 | time (s): 0.650 (total time: 33.060) Add new water r_work=0.1456 r_free=0.1801 | n_water=410 | time (s): 1.790 (total time: 34.850) Refine new water occ: r_work=0.1255 r_free=0.1588 adp: r_work=0.1247 r_free=0.1584 occ: r_work=0.1228 r_free=0.1561 adp: r_work=0.1216 r_free=0.1556 occ: r_work=0.1208 r_free=0.1552 adp: r_work=0.1198 r_free=0.1543 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1543 r_work=0.1198 r_free=0.1543 | n_water=410 | time (s): 30.420 (total time: 65.270) Filter (q & B) r_work=0.1201 r_free=0.1552 | n_water=397 | time (s): 2.220 (total time: 67.490) Filter (dist only) r_work=0.1201 r_free=0.1553 | n_water=396 | time (s): 32.200 (total time: 99.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.911166 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.178183 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1182 0.1555 0.0374 0.009 1.0 4.8 0.5 0.0 0 0.956 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.82 15.55 3.74 4.312 21.303 0.178 5.001 11.65 15.74 4.10 4.820 21.226 0.178 4.982 Individual atomic B min max mean iso aniso Overall: 6.06 106.00 20.65 4.59 1923 0 Protein: 6.06 106.00 16.84 4.59 1519 0 Water: 8.69 61.01 35.03 N/A 396 0 Other: 24.04 41.79 31.67 N/A 8 0 Chain A: 6.06 106.00 18.48 N/A 1728 0 Chain S: 17.10 61.01 39.83 N/A 195 0 Histogram: Values Number of atoms 6.06 - 16.05 1060 16.05 - 26.05 354 26.05 - 36.04 225 36.04 - 46.03 176 46.03 - 56.03 70 56.03 - 66.02 25 66.02 - 76.02 5 76.02 - 86.01 3 86.01 - 96.00 3 96.00 - 106.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1165 r_free=0.1574 r_work=0.1165 r_free=0.1576 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1165 r_free = 0.1576 target_work(ml) = 4.982 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1157 r_free = 0.1574 target_work(ml) = 4.975 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1157 r_free= 0.1574 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.975176 | | target function (ml) not normalized (work): 80767.009091 | | target function (ml) not normalized (free): 4194.066141 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1177 0.1157 0.1574 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1667 0.1655 0.1923 n_refl.: 17041 remove outliers: r(all,work,free)=0.1667 0.1655 0.1923 n_refl.: 17041 overall B=-0.43 to atoms: r(all,work,free)=0.1638 0.1626 0.1907 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1174 0.1153 0.1575 n_refl.: 17041 remove outliers: r(all,work,free)=0.1174 0.1153 0.1575 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3636 306.200 280.022 0.573 1.007 0.340 11.894-9.307 99.02 97 4 0.1847 487.209 480.743 0.910 1.007 0.327 9.237-7.194 100.00 213 7 0.1868 398.488 397.702 0.983 1.007 0.265 7.162-5.571 100.00 427 22 0.1688 299.066 293.777 0.941 1.007 0.241 5.546-4.326 100.00 867 58 0.0947 410.569 406.739 0.965 1.006 0.211 4.315-3.360 100.00 1859 96 0.0881 390.455 388.346 1.012 1.004 0.191 3.356-2.611 100.00 3867 181 0.1281 256.507 254.388 1.010 1.001 0.132 2.608-2.000 99.99 8818 434 0.1096 167.198 165.777 1.014 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1890 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1153 r_free=0.1575 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1153 r_free=0.1575 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1153 r_free=0.1575 | n_water=396 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1156 r_free=0.1579 | n_water=394 | time (s): 32.120 (total time: 32.810) Filter (q & B) r_work=0.1157 r_free=0.1580 | n_water=392 | time (s): 2.230 (total time: 35.040) Compute maps r_work=0.1157 r_free=0.1580 | n_water=392 | time (s): 0.770 (total time: 35.810) Filter (map) r_work=0.1207 r_free=0.1594 | n_water=304 | time (s): 2.160 (total time: 37.970) Find peaks r_work=0.1207 r_free=0.1594 | n_water=304 | time (s): 0.660 (total time: 38.630) Add new water r_work=0.1349 r_free=0.1719 | n_water=443 | time (s): 1.820 (total time: 40.450) Refine new water occ: r_work=0.1178 r_free=0.1515 adp: r_work=0.1170 r_free=0.1520 occ: r_work=0.1153 r_free=0.1502 adp: r_work=0.1143 r_free=0.1501 occ: r_work=0.1136 r_free=0.1499 adp: r_work=0.1128 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1128 r_free=0.1498 r_work=0.1128 r_free=0.1498 | n_water=443 | time (s): 26.150 (total time: 66.600) Filter (q & B) r_work=0.1132 r_free=0.1510 | n_water=432 | time (s): 1.890 (total time: 68.490) Filter (dist only) r_work=0.1132 r_free=0.1510 | n_water=432 | time (s): 31.550 (total time: 100.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.827839 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.153645 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1123 0.1549 0.0426 0.009 1.0 4.5 0.5 0.0 0 0.914 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.23 15.49 4.26 4.424 20.826 0.154 4.955 11.14 15.48 4.34 4.560 20.821 0.154 4.948 Individual atomic B min max mean iso aniso Overall: 5.55 104.39 20.69 4.73 1959 0 Protein: 5.55 104.39 16.38 4.72 1519 0 Water: 8.65 59.85 35.68 N/A 432 0 Other: 23.04 40.50 30.17 N/A 8 0 Chain A: 5.55 104.39 17.97 N/A 1727 0 Chain S: 17.27 59.85 40.93 N/A 232 0 Histogram: Values Number of atoms 5.55 - 15.43 1040 15.43 - 25.32 375 25.32 - 35.20 227 35.20 - 45.09 185 45.09 - 54.97 89 54.97 - 64.85 29 64.85 - 74.74 7 74.74 - 84.62 3 84.62 - 94.51 2 94.51 - 104.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.1114 r_free=0.1548 r_work=0.1114 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1114 r_free = 0.1548 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1108 r_free = 0.1548 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1108 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.943541 | | target function (ml) not normalized (work): 80253.449586 | | target function (ml) not normalized (free): 4176.319941 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1108 0.1548 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1580 0.1565 0.1903 n_refl.: 17041 remove outliers: r(all,work,free)=0.1580 0.1565 0.1903 n_refl.: 17041 overall B=-0.28 to atoms: r(all,work,free)=0.1563 0.1548 0.1895 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1127 0.1106 0.1544 n_refl.: 17041 remove outliers: r(all,work,free)=0.1127 0.1106 0.1544 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3543 306.200 281.961 0.570 1.001 0.340 11.894-9.307 99.02 97 4 0.1778 487.209 478.589 0.912 1.002 0.330 9.237-7.194 100.00 213 7 0.1811 398.488 398.067 0.988 1.002 0.230 7.162-5.571 100.00 427 22 0.1558 299.066 292.759 0.941 1.002 0.210 5.546-4.326 100.00 867 58 0.0923 410.569 406.898 0.968 1.002 0.185 4.315-3.360 100.00 1859 96 0.0856 390.455 388.556 1.008 1.002 0.181 3.356-2.611 100.00 3867 181 0.1226 256.507 254.195 1.002 1.001 0.063 2.608-2.000 99.99 8818 434 0.1046 167.198 165.956 0.998 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9680 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1106 r_free=0.1544 After: r_work=0.1107 r_free=0.1543 ================================== NQH flips ================================== r_work=0.1107 r_free=0.1543 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1107 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1107 r_free=0.1543 | n_water=432 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1107 r_free=0.1539 | n_water=431 | time (s): 35.040 (total time: 35.690) Filter (q & B) r_work=0.1108 r_free=0.1539 | n_water=430 | time (s): 1.600 (total time: 37.290) Compute maps r_work=0.1108 r_free=0.1539 | n_water=430 | time (s): 0.720 (total time: 38.010) Filter (map) r_work=0.1190 r_free=0.1552 | n_water=336 | time (s): 2.260 (total time: 40.270) Find peaks r_work=0.1190 r_free=0.1552 | n_water=336 | time (s): 0.660 (total time: 40.930) Add new water r_work=0.1311 r_free=0.1644 | n_water=478 | time (s): 1.850 (total time: 42.780) Refine new water occ: r_work=0.1146 r_free=0.1501 adp: r_work=0.1139 r_free=0.1506 occ: r_work=0.1122 r_free=0.1485 adp: r_work=0.1113 r_free=0.1490 occ: r_work=0.1106 r_free=0.1479 adp: r_work=0.1099 r_free=0.1481 ADP+occupancy (water only), MIN, final r_work=0.1099 r_free=0.1481 r_work=0.1099 r_free=0.1481 | n_water=478 | time (s): 30.040 (total time: 72.820) Filter (q & B) r_work=0.1104 r_free=0.1493 | n_water=466 | time (s): 1.860 (total time: 74.680) Filter (dist only) r_work=0.1104 r_free=0.1494 | n_water=465 | time (s): 36.850 (total time: 111.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.159119 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.187388 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1120 0.1524 0.0404 0.010 1.1 8.6 0.5 0.0 0 1.080 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.20 15.24 4.04 4.459 20.667 0.187 4.945 11.10 15.19 4.10 4.605 20.747 0.187 4.940 Individual atomic B min max mean iso aniso Overall: 4.98 104.27 20.89 5.07 1992 0 Protein: 4.98 104.27 16.12 5.06 1519 0 Water: 8.16 64.85 36.30 N/A 465 0 Other: 22.65 37.68 29.91 N/A 8 0 Chain A: 4.98 104.27 17.72 N/A 1727 0 Chain S: 18.50 64.85 41.51 N/A 265 0 Histogram: Values Number of atoms 4.98 - 14.91 1023 14.91 - 24.83 392 24.83 - 34.76 220 34.76 - 44.69 204 44.69 - 54.62 101 54.62 - 64.55 37 64.55 - 74.48 6 74.48 - 84.41 4 84.41 - 94.34 2 94.34 - 104.27 3 =========================== Idealize ADP of riding H ========================== r_work=0.1110 r_free=0.1519 r_work=0.1109 r_free=0.1519 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1109 r_free = 0.1519 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1518 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1103 r_free= 0.1518 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.935461 | | target function (ml) not normalized (work): 80122.269040 | | target function (ml) not normalized (free): 4164.857404 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1126 0.1454 5.4681 5.6967| | 2: 3.63 - 2.88 1.00 2711 122 0.1084 0.1506 5.2261 5.3476| | 3: 2.88 - 2.52 1.00 2681 148 0.1346 0.1664 5.136 5.2043| | 4: 2.52 - 2.29 1.00 2661 139 0.0917 0.1474 4.6159 4.9589| | 5: 2.29 - 2.13 1.00 2678 122 0.0953 0.1451 4.5721 4.8473| | 6: 2.13 - 2.00 1.00 2692 117 0.1121 0.1677 4.5642 4.7502| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2811 159 0.94 9.31 1.00 0.95 6591.88| | 2: 3.63 - 2.88 2711 122 0.92 13.18 1.01 0.95 6591.88| | 3: 2.88 - 2.52 2681 148 0.87 19.41 0.99 0.95 6591.88| | 4: 2.52 - 2.29 2661 139 0.93 12.03 1.01 0.97 2078.28| | 5: 2.29 - 2.13 2678 122 0.92 13.95 1.00 0.97 2078.28| | 6: 2.13 - 2.00 2692 117 0.90 16.70 0.99 0.97 2078.28| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2078.28 max = 6591.88 mean = 4358.99| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.77 mean = 14.06| |phase err.(test): min = 0.00 max = 89.10 mean = 13.78| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1123 0.1103 0.1518 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1549 0.1532 0.1886 n_refl.: 17041 remove outliers: r(all,work,free)=0.1549 0.1532 0.1886 n_refl.: 17041 overall B=-0.22 to atoms: r(all,work,free)=0.1536 0.1519 0.1877 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1103 0.1519 n_refl.: 17041 remove outliers: r(all,work,free)=0.1123 0.1103 0.1519 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3572 306.200 283.090 0.561 1.003 0.334 11.894-9.307 99.02 97 4 0.1766 487.209 479.248 0.913 1.004 0.330 9.237-7.194 100.00 213 7 0.1745 398.488 398.893 0.984 1.005 0.222 7.162-5.571 100.00 427 22 0.1565 299.066 292.849 0.941 1.005 0.220 5.546-4.326 100.00 867 58 0.0931 410.569 406.687 0.963 1.004 0.175 4.315-3.360 100.00 1859 96 0.0871 390.455 388.323 1.002 1.003 0.171 3.356-2.611 100.00 3867 181 0.1235 256.507 254.248 0.999 1.000 0.063 2.608-2.000 99.99 8818 434 0.1028 167.198 165.880 0.992 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7588 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2783 0.1849 0.083 5.466 8.8 119.3 19.9 258 0.000 1_bss: 0.1608 0.1647 0.083 5.466 8.4 118.9 19.5 258 0.000 1_settarget: 0.1608 0.1647 0.083 5.466 8.4 118.9 19.5 258 0.000 1_nqh: 0.1609 0.1648 0.083 5.466 8.4 118.9 19.5 258 0.003 1_weight: 0.1609 0.1648 0.083 5.466 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1352 0.1643 0.009 0.968 8.4 118.9 19.5 258 0.158 1_adp: 0.1276 0.1667 0.009 0.968 6.5 113.9 20.0 258 0.158 1_regHadp: 0.1279 0.1674 0.009 0.968 6.5 113.9 20.0 258 0.158 1_occ: 0.1273 0.1665 0.009 0.968 6.5 113.9 20.0 258 0.158 2_bss: 0.1272 0.1662 0.009 0.968 6.1 113.5 19.6 258 0.158 2_settarget: 0.1272 0.1662 0.009 0.968 6.1 113.5 19.6 258 0.158 2_updatecdl: 0.1272 0.1662 0.009 0.990 6.1 113.5 19.6 258 0.158 2_nqh: 0.1272 0.1663 0.009 0.990 6.1 113.5 19.6 258 0.155 2_sol: 0.1237 0.1559 0.009 0.990 6.1 112.7 20.9 355 n/a 2_weight: 0.1237 0.1559 0.009 0.990 6.1 112.7 20.9 355 n/a 2_xyzrec: 0.1213 0.1589 0.008 0.923 6.1 112.7 20.9 355 n/a 2_adp: 0.1201 0.1615 0.008 0.923 6.3 107.7 21.3 355 n/a 2_regHadp: 0.1203 0.1616 0.008 0.923 6.3 107.7 21.3 355 n/a 2_occ: 0.1200 0.1613 0.008 0.923 6.3 107.7 21.3 355 n/a 3_bss: 0.1193 0.1605 0.008 0.923 5.8 107.1 20.8 355 n/a 3_settarget: 0.1193 0.1605 0.008 0.923 5.8 107.1 20.8 355 n/a 3_updatecdl: 0.1193 0.1605 0.008 0.920 5.8 107.1 20.8 355 n/a 3_nqh: 0.1193 0.1605 0.008 0.920 5.8 107.1 20.8 355 n/a 3_sol: 0.1201 0.1553 0.008 0.920 5.8 107.1 20.8 396 n/a 3_weight: 0.1201 0.1553 0.008 0.920 5.8 107.1 20.8 396 n/a 3_xyzrec: 0.1182 0.1555 0.009 0.967 5.8 107.1 20.8 396 n/a 3_adp: 0.1165 0.1574 0.009 0.967 6.1 106.0 20.6 396 n/a 3_regHadp: 0.1165 0.1576 0.009 0.967 6.1 106.0 20.6 396 n/a 3_occ: 0.1157 0.1574 0.009 0.967 6.1 106.0 20.6 396 n/a 4_bss: 0.1153 0.1575 0.009 0.967 5.6 105.6 20.2 396 n/a 4_settarget: 0.1153 0.1575 0.009 0.967 5.6 105.6 20.2 396 n/a 4_updatecdl: 0.1153 0.1575 0.009 0.967 5.6 105.6 20.2 396 n/a 4_nqh: 0.1153 0.1575 0.009 0.967 5.6 105.6 20.2 396 n/a 4_sol: 0.1132 0.1510 0.009 0.967 5.6 105.6 20.7 432 n/a 4_weight: 0.1132 0.1510 0.009 0.967 5.6 105.6 20.7 432 n/a 4_xyzrec: 0.1123 0.1549 0.009 0.959 5.6 105.6 20.7 432 n/a 4_adp: 0.1114 0.1548 0.009 0.959 5.5 104.4 20.7 432 n/a 4_regHadp: 0.1114 0.1548 0.009 0.959 5.5 104.4 20.7 432 n/a 4_occ: 0.1108 0.1548 0.009 0.959 5.5 104.4 20.7 432 n/a 5_bss: 0.1106 0.1544 0.009 0.959 5.3 104.1 20.4 432 n/a 5_settarget: 0.1106 0.1544 0.009 0.959 5.3 104.1 20.4 432 n/a 5_updatecdl: 0.1106 0.1544 0.009 0.960 5.3 104.1 20.4 432 n/a 5_setrh: 0.1107 0.1543 0.009 0.960 5.3 104.1 20.4 432 n/a 5_nqh: 0.1107 0.1543 0.009 0.960 5.3 104.1 20.4 432 n/a 5_sol: 0.1104 0.1494 0.009 0.960 5.3 104.1 20.7 465 n/a 5_weight: 0.1104 0.1494 0.009 0.960 5.3 104.1 20.7 465 n/a 5_xyzrec: 0.1120 0.1524 0.010 1.098 5.3 104.1 20.7 465 n/a 5_adp: 0.1110 0.1519 0.010 1.098 5.0 104.3 20.9 465 n/a 5_regHadp: 0.1109 0.1519 0.010 1.098 5.0 104.3 20.9 465 n/a 5_occ: 0.1103 0.1518 0.010 1.098 5.0 104.3 20.9 465 n/a end: 0.1103 0.1519 0.010 1.098 4.8 104.1 20.7 465 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3495505_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3495505_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1200 Refinement macro-cycles (run) : 946.5500 Write final files (write_after_run_outputs) : 19.3400 Total : 969.0100 Total CPU time: 16.50 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:31 PST -0800 (1735494091.66 s) Start R-work = 0.1608, R-free = 0.1647 Final R-work = 0.1103, R-free = 0.1519 =============================================================================== Job complete usr+sys time: 1009.99 seconds wall clock time: 17 minutes 13.39 seconds (1033.39 seconds total)